Tree Breeding Tools Arker assisted selection Dag Lindgren

Tree Breeding Tools “Arker assisted selection” Dag Lindgren Presentation in Finland 01 -03 -24

Website http: //www. genfys. slu. se/staff/dagl contains: • Documents • Documentation • Newsletter • Thesis • Research group • Research targets • Teaching • Links • Home page • Tree Breeding Tools

Tree Breeding Tools • Downloadable programs • by Dag L and collaborators • many EXCEL worksheets (“ark” or “arkki”) • Tutorial tools • Seldom about characters or data

Why Tree Breeding Tools? Think first!!! ing d e re b I Notes: common sense is also useful! Garbage in = garbage out!

Why Worksheets? • Transparent relations • Works on most computers • Place for lots of explanation • Easy to change and update • Customers can develop and adjust the tool • Formula collection • Own training

Central factors in tree breeding • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity More gain! More diversity ! Faster ! Cheaper ! • Time • Cost • Technique Conflicting goals!!

Environment description • Temperature climate • Light climate

Temperature climate TEMPPRED. EXE • Average temperature in Sweden and Finland • Accumulated heat sums • From official stations representative forest land 1961 -1990

N len ight g tem th a p i nd s. . . Example: Conf site: Mekrijärvi 62° 46’N 30° 59’E 150 m asl March 24, 2001 Note: Outcome indicated program is about as reliable as Finnish weather forcast service

Light climate Dag. L. exe • Returns night length as a function of date, place and night criteria.

Environment -adaptation ADAPTATION. XLS • Plantations site and seed source value • Flexibility of seed source • Seed orchards have gain and wider adaptation! • Choose zone size!

Environment -adaptation Systematic G*E Plantation sites and seed origins described by a single value Flexibility (C) of seed source Performance Cauchy function 1 A C B 0 Site type value

Environment -adaptation Wider zones = more maladaptation Performance (max=1) Performance as a function of zone size 1. 2 1. 0 0. 8 0. 6 0. 4 at zone periphery 0. 2 average over zone 0 0 0. 2 0. 4 For Scots pine a flex unit is around 3 lat 0. 6 0. 8 Zone size (flex units) 1 1. 2

Environment G*E for Random sites How many for testing clones or progenies? sites 2001. xls • Given: the range of environment • Inputs: Available resources cost per plant and per site VG*E VP within site and entry • Results: number of plant/site and sites Efficiency

Central factors in tree breeding • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique

Selection in normaldist SELEINT. EXE; SELENOR. EXE • Selection intensity, i , proportional to gain • Variance in truncation selected proportion

Selection in N(0, 1) 0. 4 selection intensity 0. 2 truncation point variation 0. 0 -3. 0 0. 0 3. 0

Central factors in tree breeding • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique

Gene diversity! Ark=feature to conserve diversity

Group coancestry • Average coancestry including self-coancestry (“genomsnittligt släktskap”) • Coancestry genes IBD, gene diversity = genes not identical. • Loss of gene diversity = group coancestry • Needs a reference (“source” or “wild”, as inbreeding or coancestry does)

Status number • Effective number • Gene diversity loss - number with the same loss • The same cumulated drift of gene frequencies (cf variance effective number, per generation) • Inbreeding - number which at random mating produces as much inbreeding

Status number status. exe • Input a text file with genotypes and their pedigree tracking back to founders • Returns status number • Made by Gea, Jefferson and Weaver, New Zealand

Group coancestry_matrix. xls • Tutorial, simple pedigree, but transparent mother aunt uncle sister cousin What is the group coancestry of this ”family”?

Gene drop analyses retention. xls • “Drops” founder genes through a geneology • Returns the probability that different numbers remains • By Leopoldo Sanchez-Rodrigues

Central factors in tree breeding joint consideration • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique Linear Deployment Group Merit Selection

Linear deployment • Maximises gain at given gene diversity Frequency, Proportion • It is optimal to deploy genetic materials linearly related to their breeding value Linear deployment g 0 (intercept) b (slope) Performance = Breeding Value

Linear deployment Linear Deploymen 2000. xls Performance= Breeding Value • Any line is a solution, the question is to what problem Linear deployment b (slope) g 0 (intercept) Frequency, Proportion

Linear deployment Frequency, Proportion • Works also with constraint (genetic thinning of seed orchards) Linear deployment with constraint Performance

Linear deployment selenor 3. exe • General “optimal” linear deployment solutions for normal distribution

Group Merit Selection Coa. Demo. xls • For demonstration • By Zheng&Lindgren • Input: five candidates • Selects three, which maximises the average of breeding value and group coancestry

Group Merit Selection tool • By Thuy Olsson • Windows oriented, unpack and install • Input: files with candidates and weight of gain versus diversity • Output: A group which maximises the average of breeding value and group coancestry

Orchard Manager orchard_management. xls • By Kang and Lindgren

Central factors in tree breeding - joint consideration • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique Gain predictor Breeding cycler

Gain predictor Gainpred. xls • Predicts actually much more than gain • Linear, short-term. ”Starts with plus trees and ends with a seed orchard”

Breeding cycler Breeding_cycle. xls • By Danusevicius and Lindgren • Long-term cyclic breeding

Tutorials • Mini course on quantitative genetics • Examples

Message from a senior professor of Forest Genetics At least one week attention on the concepts behind TBT is needed each five years • For all who call them-selves forest tree breeders • For all who get the doctors title in forest genetics in the future • For most professional forest geneticists

End of slide show - Time for sauna! I br ee di ng